188 Transcription Overview: The Basic Mechanism of RNA Synthesis

There are 3 main kinds of RNA, messenger, ribosomal and transfer RNA. The transcription of any kind of RNA occurs in 3 steps, called initiation, elongation and termination. We’ll learn about promoters which are the start sites of transcription. We’ll look a little bit at prokaryotic and eukaryotic transcription and RNA processing by cleavage (which is to say simply hydrolysis of pieces of unwanted RNA), splicing (the removal of intervening sequences or introns in messenger RNA), and then, nucleotide additions or base modifications, the sorts of things that happen with transfer RNAs. So there are 3 main kinds of cellular RNA, the mRNA, the rRNA (which is part of the ribosome structure and as you’ll see, has enzymatic function independent of polypeptide structure), and then, transfer RNA. This is what makes up most of the cell’s RNA. There are other kinds of RNA. And as an example, primers are a kind of RNA as well, but they and other kinds of RNAs, quantitatively, are not a major component of a cell’s RNA. So this is transcription as it would occur in all cells. And the first part of course, the first step is initiation. And what we see here first of all is a double-stranded DNA, two lines representing two strands of DNA that are to be transcribed. There is a promoter to the left in blue, the right arrow which represents the start site of transcription, and then this red RNA polymerase. The RNA polymerase binds to the promoter, recognizes the sequence of the promoter and is thereby positioned at the start site of transcription. Once that happens it is possible to start growing an RNA molecule by elongation, a series of cyclic reactions during which an RNA is produced, beginning at the 5′ end of the RNA, and growing towards the 3′ end. The precursors are the nucleotide triphosphates (NTPs), specifically for RNA. Those of course are: ATP, UTP, CTP and GTP. So one of those is going to be added next based on the base that’s in the template strand that’s being transcribed. The result will be to create a nucleotide monophosphate chain that is n+1. nucleotides. Each new addition is accompanied by the hydrolysis of a pyrophosphate, two phosphates, off the end of the nucleotide as the nucleotide is added to the new chain by a condensation reaction. Not shown here is the fact that water comes out of this reaction. Elongation then, just continues 5′ to 3′ until termination. The RNA polymerase reaches a termination site, at which point the RNA is freed up. You should have seen in this set of animations, that the DNA is in fact, unwinding during transcription, but that immediately behind the RNA that is being produced, the DNA rewinds. This is a major difference between replication by a DNA polymerase and transcription by an RNA polymerase. During replication you will recall, once the DNA is unwound and a new strand of DNA is produced, the new strand in the old strand in semiconservative fashion, remain associated. So clearly the RNA does not remain permanently associated with its template strand. It does remain associated for few nucleotides, but then quickly separates. So you can see at the bottom of this illustration, most of the RNA is in fact free of any DNA associations. In a double-stranded chromosomal DNA molecule, whether it’s bacterial or eukaryotic, genes can face in different directions, which means the template strand can sometimes be, in this example, the upper strand, and sometimes the lower strand. And so we have an illustration of several regions of DNA. Shown in blue are the directions of transcription of different genes, arbitrarily labeled a, b, c, d and so on. The promoters are shown as little greenish arrows and I’ve indicated those in the illustration. So each gene has a promoter and the promoter faces in the correct direction for the gene to be transcribed.

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